Yes you can do this without needing any other changes. Ff14SB also has
significant side chain updates beyond the backbone ones you mentioned. I
strongly recommend it over ff99SB.
On Nov 4, 2016 11:09 AM, "Eric Lang" <eric.lang.bristol.ac.uk> wrote:
> Hello,
>
> I am going to run some pH-REMD simulations in explicit solvent of an
> helical protein.
>
> I understand that CpHMD, and by extension pH-REMD, are parametrised with
> ff10 (equivalent to the ff99SB force field used in the original Mongan
> paper).
>
> However, since my structure is composed solely of alpha helices, I am
> concerned about the tendency of ff99SB (and ff10) to under-stabilise alpha
> helices and thus model an unrealistic partial unfolding of the helices.
>
> I understand that ff14SB has some updated torsion terms for Phi and Psi
> angles to improve the accuracy of alpha helix simulations.
>
> Could I therefore use ff14SB instead of ff10 to run my CpHMD without
> problems or would this require to re-calculate the model compounds pKa,
> update the parameters for the ionisable residues, and perhaps other things?
>
> I am not familiar enough with the Amber force fields, so I am not able to
> judge how different ff14SB is from ff10, but since the original method was
> developed with ff99SB and we now use ff10 for this method, is it a really
> big change for the constant pH calculations, to shift to ff14SB?
>
> If only the parameters for the ionisable residues need to be updated, is it
> a big task or could it be done easily, would you please be able to give me
> some indication about a possible procedure to do this? (sorry, again if
> this is a naive question but I am more familiar with Charmm force fields
> than with Amber ones).
>
> Many thanks in advance for your help,
>
> Eric
>
> --
>
> Eric Lang
>
> BrisSynBio Postdoctoral Research Associate Modelling
> Centre for Computational Chemistry
> School of Chemistry - University of Bristol
> Bristol BS8 1TS - United Kingdom
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Received on Fri Nov 04 2016 - 08:30:02 PDT
